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#2320 closed defect (fixed)

ISOLDE/ChimeraX 0.8 errors

Reported by:	ash@…	Owned by:	Tristan Croll
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-4.15.0-48-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.8 (2018-12-17)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/installed.py", line 270, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  

> toolshed show ISOLDE

> open /u/azsha/AS/CVI03/Buster/LoopC_test_120819/refine_all_140819.pdb

Summary of feedback from opening
/u/azsha/AS/CVI03/Buster/LoopC_test_120819/refine_all_140819.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK --------------------- added by autoBUSTER
-------------------------------  
  
Ignored bad PDB record found on line 2  
REMARK run at = Mon Aug 12 10:28:08 CEST 2019  
  
Ignored bad PDB record found on line 14  
REMARK Files used:  
  
Ignored bad PDB record found on line 15  
REMARK PDB = /u/azsha/AS/CVI03/Buster/LoopC_test_120819/pdbchk.pd  
  
Ignored bad PDB record found on line 16  
REMARK MTZ = /u/azsha/AS/CVI03/090819/xscale_CVI03Sy7_merged_p21_  
  
45 messages similar to the above omitted  
  
Chain information for refine_all_140819.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for refine_all_140819.pdb  
---  
Chain | Description  
1.3/A | No description available  
1.3/B | No description available  
1.3/C | No description available  
  

> toolshed show ISOLDE

Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1179, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1206, in add_xtal_data  
xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/map_mgr.py", line 239, in add_xmapset_from_mtz  
return XmapSet(self, mtzdata)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 169, in __init__  
choice = self._choose_fsigf(crystal_data)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 453, in _choose_fsigf  
choice = _f_sigf_chooser(list(fsigfs.keys()))  
NameError: name '_f_sigf_chooser' is not defined  
  
NameError: name '_f_sigf_chooser' is not defined  
  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 453, in _choose_fsigf  
choice = _f_sigf_chooser(list(fsigfs.keys()))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1179, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1206, in add_xtal_data  
xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/map_mgr.py", line 239, in add_xmapset_from_mtz  
return XmapSet(self, mtzdata)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 169, in __init__  
choice = self._choose_fsigf(crystal_data)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 453, in _choose_fsigf  
choice = _f_sigf_chooser(list(fsigfs.keys()))  
NameError: name '_f_sigf_chooser' is not defined  
  
NameError: name '_f_sigf_chooser' is not defined  
  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 453, in _choose_fsigf  
choice = _f_sigf_chooser(list(fsigfs.keys()))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1179, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1206, in add_xtal_data  
xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/map_mgr.py", line 239, in add_xmapset_from_mtz  
return XmapSet(self, mtzdata)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 169, in __init__  
choice = self._choose_fsigf(crystal_data)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 453, in _choose_fsigf  
choice = _f_sigf_chooser(list(fsigfs.keys()))  
NameError: name '_f_sigf_chooser' is not defined  
  
NameError: name '_f_sigf_chooser' is not defined  
  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 453, in _choose_fsigf  
choice = _f_sigf_chooser(list(fsigfs.keys()))  
  
See log for complete Python traceback.  
  

> toolshed show ISOLDE

Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Adding hydrogens  
No usable SEQRES records for refine_all_140819.pdb (#1.3) chain A; guessing
termini instead  
No usable SEQRES records for refine_all_140819.pdb (#1.3) chain B; guessing
termini instead  
No usable SEQRES records for refine_all_140819.pdb (#1.3) chain C; guessing
termini instead  
Chain-initial residues that are actual N termini: /A ALA 16, /B GLN 1, /C ALA
7  
Chain-initial residues that are not actual N termini: /A ALA 154, /A PHE 175,
/A ALA 209, /A LYS 251, /A TYR 495  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ALA 525, /A TYR 128, /A
ALA 172, /A LYS 202, /A ALA 246, /A THR 491, /B SER 120, /C ALA 19  
432 hydrogen bonds  
Adding 'H' to /A ALA 154  
Adding 'H' to /A PHE 175  
Adding 'H' to /A ALA 209  
Adding 'H' to /A LYS 251  
Adding 'H' to /A TYR 495  
/A ALA 525 is not terminus, removing H atom from 'C'  
/A TYR 128 is not terminus, removing H atom from 'C'  
/A ALA 172 is not terminus, removing H atom from 'C'  
/A LYS 202 is not terminus, removing H atom from 'C'  
/A ALA 246 is not terminus, removing H atom from 'C'  
/A THR 491 is not terminus, removing H atom from 'C'  
/B SER 120 is not terminus, removing H atom from 'C'  
/C ALA 19 is not terminus, removing H atom from 'C'  
4647 hydrogens added  
Bad residue number: 449  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 24 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 42 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 60 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 92 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 139 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 149 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 208 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 225 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 236 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 306 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 370 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 372 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 402 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 446 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYX does not match the residue 478 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYX does not match the residue 551 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (ALA). The set of atoms is similar
to ALA, but it is missing 5 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (GLU). The set of atoms is similar
to GLU, but it is missing 6 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (PHE). The set of atoms is similar
to PHE, but it is missing 9 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (VAL). The set of atoms is similar
to PRO, but it is missing 7 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (LEU). The set of atoms is similar
to HID, but it is missing 9 atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (THR). The set of atoms is similar
to ASP, but it is missing 5 atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (SER). The set of atoms is similar
to SER, but it is missing 5 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (VAL). The set of atoms is similar
to PRO, but it is missing 7 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 449 (LIG). This might mean your
input topology is missing some atoms or bonds, or possibly that you are using
the wrong force field.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1079, in _model_changes_cb  
self._update_iffy_rota_list()  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2203, in _update_iffy_rota_list  
table.setRowCount(0)  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QTableWidget
has been deleted:  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2203, in _update_iffy_rota_list  
table.setRowCount(0)  
  
See log for complete Python traceback.  
  
Adding hydrogens  
No usable SEQRES records for refine_all_140819.pdb (#1.3) chain A; guessing
termini instead  
No usable SEQRES records for refine_all_140819.pdb (#1.3) chain B; guessing
termini instead  
No usable SEQRES records for refine_all_140819.pdb (#1.3) chain C; guessing
termini instead  
Chain-initial residues that are actual N termini: /A ALA 16, /B GLN 1, /C ALA
7  
Chain-initial residues that are not actual N termini: /A ALA 154, /A PHE 175,
/A ALA 209, /A LYS 251, /A TYR 495  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ALA 525, /A TYR 128, /A
ALA 172, /A LYS 202, /A ALA 246, /A THR 491, /B SER 120, /C ALA 19  
409 hydrogen bonds  
/A ALA 525 is not terminus, removing H atom from 'C'  
/A TYR 128 is not terminus, removing H atom from 'C'  
/A ALA 172 is not terminus, removing H atom from 'C'  
/A LYS 202 is not terminus, removing H atom from 'C'  
/A ALA 246 is not terminus, removing H atom from 'C'  
/A THR 491 is not terminus, removing H atom from 'C'  
/B SER 120 is not terminus, removing H atom from 'C'  
/C ALA 19 is not terminus, removing H atom from 'C'  
0 hydrogens added  
Bad residue number: 449  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 24 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 42 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 60 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 92 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 139 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 149 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 208 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 225 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 236 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 306 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 370 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 372 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 402 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 446 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYX does not match the residue 478 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYX does not match the residue 551 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (ALA). The set of atoms is similar
to ALA, but it is missing 5 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (GLU). The set of atoms is similar
to GLU, but it is missing 6 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (PHE). The set of atoms is similar
to PHE, but it is missing 9 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (VAL). The set of atoms is similar
to PRO, but it is missing 7 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (LEU). The set of atoms is similar
to HID, but it is missing 9 atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (THR). The set of atoms is similar
to ASP, but it is missing 5 atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (SER). The set of atoms is similar
to SER, but it is missing 5 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (VAL). The set of atoms is similar
to PRO, but it is missing 7 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 449 (LIG). This might mean your
input topology is missing some atoms or bonds, or possibly that you are using
the wrong force field.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 449 (LIG). This might mean your
input topology is missing some atoms or bonds, or possibly that you are using
the wrong force field.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1079, in _model_changes_cb  
self._update_iffy_rota_list()  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2203, in _update_iffy_rota_list  
table.setRowCount(0)  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QTableWidget
has been deleted:  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2203, in _update_iffy_rota_list  
table.setRowCount(0)  
  
See log for complete Python traceback.  
  
Adding hydrogens  
No usable SEQRES records for refine_all_140819.pdb (#1.3) chain A; guessing
termini instead  
No usable SEQRES records for refine_all_140819.pdb (#1.3) chain B; guessing
termini instead  
No usable SEQRES records for refine_all_140819.pdb (#1.3) chain C; guessing
termini instead  
Chain-initial residues that are actual N termini: /A ALA 16, /B GLN 1, /C ALA
7  
Chain-initial residues that are not actual N termini: /A ALA 154, /A PHE 175,
/A ALA 209, /A LYS 251, /A TYR 495  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ALA 525, /A TYR 128, /A
ALA 172, /A LYS 202, /A ALA 246, /A THR 491, /B SER 120, /C ALA 19  
409 hydrogen bonds  
/A ALA 525 is not terminus, removing H atom from 'C'  
/A TYR 128 is not terminus, removing H atom from 'C'  
/A ALA 172 is not terminus, removing H atom from 'C'  
/A LYS 202 is not terminus, removing H atom from 'C'  
/A ALA 246 is not terminus, removing H atom from 'C'  
/A THR 491 is not terminus, removing H atom from 'C'  
/B SER 120 is not terminus, removing H atom from 'C'  
/C ALA 19 is not terminus, removing H atom from 'C'  
0 hydrogens added  
Bad residue number: 449  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 24 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 42 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 60 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 92 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 139 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 149 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 208 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 225 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 236 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 306 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 370 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 372 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 402 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 446 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYX does not match the residue 478 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1095, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYX does not match the residue 551 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (ALA). The set of atoms is similar
to ALA, but it is missing 5 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (GLU). The set of atoms is similar
to GLU, but it is missing 6 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (PHE). The set of atoms is similar
to PHE, but it is missing 9 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (VAL). The set of atoms is similar
to PRO, but it is missing 7 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (LEU). The set of atoms is similar
to HID, but it is missing 9 atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (THR). The set of atoms is similar
to ASP, but it is missing 5 atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (SER). The set of atoms is similar
to SER, but it is missing 5 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (VAL). The set of atoms is similar
to PRO, but it is missing 7 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 449 (LIG). This might mean your
input topology is missing some atoms or bonds, or possibly that you are using
the wrong force field.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 449 (LIG). This might mean your
input topology is missing some atoms or bonds, or possibly that you are using
the wrong force field.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 570, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1196, in __init__  
sim_params, residue_templates)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1292, in
_create_openmm_system  
return forcefield.createSystem(top, **system_params)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/simtk/openmm/app/forcefield.py", line 1128, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 449 (LIG). This might mean your
input topology is missing some atoms or bonds, or possibly that you are using
the wrong force field.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1079, in _model_changes_cb  
self._update_iffy_rota_list()  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2203, in _update_iffy_rota_list  
table.setRowCount(0)  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QTableWidget
has been deleted:  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2203, in _update_iffy_rota_list  
table.setRowCount(0)  
  
See log for complete Python traceback.  
  
Excluding residue  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1179, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1206, in add_xtal_data  
xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/map_mgr.py", line 239, in add_xmapset_from_mtz  
return XmapSet(self, mtzdata)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 158, in __init__  
self.expand_to_cover_coords(self.master_map_mgr.last_covered_selection, 10)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 473, in
expand_to_cover_coords  
get_minmax_grid(coords, cell, grid)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/clipper_util.py", line 78, in get_minmax_grid  
return _util.get_minmax_grid(coords, cell, grid_sampling)  
TypeError: get_minmax_grid(): incompatible function arguments. The following
argument types are supported:  
1\. (arg0: numpy.ndarray[float64], arg1: chimerax.clipper.clipper_python.Cell,
arg2: chimerax.clipper.clipper_python.Grid_sampling) -> numpy.ndarray[int32]  
  
Invoked with: <chimerax.atomic.molarray.Atoms object at 0x7fd1e9135ba8>,
<chimerax.clipper.clipper_python.Cell object at 0x7fd2058abf10>,
<chimerax.clipper.clipper_python.Grid_sampling object at 0x7fd2058ab5a8>  
  
TypeError: get_minmax_grid(): incompatible function arguments. The following
argument types are supported:  
1\. (arg0: numpy.ndarray[float64], arg1: chimerax.clipper.clipper_python.Cell,
arg2: chimerax.clipper.clipper_python.Grid_sampling) -> numpy.ndarray[int32]  
  
Invoked with: , ,  
  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/clipper_util.py", line 78, in get_minmax_grid  
return _util.get_minmax_grid(coords, cell, grid_sampling)  
  
See log for complete Python traceback.  
  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/chimerax/core/updateloop.py", line 72, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 159, in draw  
self._draw_scene(camera, drawings)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 227, in _draw_scene  
draw_highlight_outline(r, highlight_drawings)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 1416, in
draw_highlight_outline  
r.outline.finish_rendering_outline()  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/chimerax/core/graphics/opengl.py", line 1574, in
finish_rendering_outline  
r.pop_framebuffer()  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/chimerax/core/graphics/opengl.py", line 564, in pop_framebuffer  
fb.activate()  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-
packages/chimerax/core/graphics/opengl.py", line 1824, in activate  
GL.glDrawBuffer(self._draw_buffer)  
File "errorchecker.pyx", line 53, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
(src/errorchecker.c:1218)  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_BACK,)  
)  
  




OpenGL version: 3.3.0 NVIDIA 418.40.04
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by Tristan Croll, 6 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ISOLDE/ChimeraX 0.8 errors

comment:2 by Tristan Croll, 6 years ago

Resolution:	→ fixed
Status:	assigned → closed

The errors listed here also should be fixed in the latest ISOLDE versions.

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